2.09                      ******************
                                  * MRGDF WRITE-UP *
                                  ******************
        
           MRGDF is a program to create coefficients for difference or 
        cross-difference Fourier synthesis calculations, i.e. try to solve a 
        new derivative from phase information obtained from one or more other 
        derivatives. It can also be used simply to search for additional heavy 
        atom sites once initial estimates of protein phases become available,
        although the "difference coefficients" file output from PHASIT may
        be better suited in this case since one can then also subtract out
        the heavy atoms already present in the model, and also generate a
        "calculated" Patterson for comparison with the "observed" one. The
        program is interactive and prompts for the names of the input and
        output files, and a d spacing cutoff. The output file can be used in 
        FSFOUR with MAPTYP=3 to compute the difference or the cross-difference 
        Fourier synthesis.  If the input derivative file is one of the 
        "merged" data files originally input to PHASIT, then the coefficients 
        output can be used to compute a difference Fourier to identify other 
        heavy atom sites which may have been overlooked. In that case it is 
        not a "cross-difference" Fourier but a straight difference Fourier. 
        Program PSRCH can be used to list the strongest peaks in the map. The 
        program will also prompt the user to supply values for derivative to 
        native scale and delta B factors, if rescaling is requested. If 
        utilized, this option enables the user to change the scaling 
        originally carried out in CMBISO, to reflect the fact that additional 
        scattering power is present in the derivative data set. In that case 
        the new scaling parameters should be those determined from PHASIT in 
        phase refinement mode.  
        
                                      ***** FILES *****
        
        The input scaled data file is identical (in form) to the isomorphous 
        "merged" data file input to PHASIT. Each record should contain
        
        H, K, L, FP, SIG(FP), FPH, SIG(FPH)
        
        with FP and FPH already properly scaled together as in CMBISO. This 
        file refers to the new derivative which is to be solved, or to a 
        current derivative for which one wants to search for additional heavy 
        atom sites. It is read in free format.
        
        The input protein phase file can be one of two types. Usually it will 
        be the last output file from BNDRY, or an output file from PHASIT (in 
        protein phasing mode). In general, it should contain the best 
        available phases. The form of the file would then be identical to that 
        output from BNDRY or PHASIT (in protein phasing mode). It is also 
        possible however, to input a protein phase file which contains records 
        with the "short" reflection file form (only h,k,l,fo,fc,phi) as 
        generated by GREF or PHASIT (in structure factor calculation mode with 
        IHLCF=0). In that case there is no figure of merit present, thus FOM= 
        1. is used during generation of the output coefficients. This would be 
        the case if the protein phases come from a complete (or partial) 
        protein model based structure factor calculation. The program can 
        automatically determine which type of file was input. Note however,
        that a protein phase file generated by GREF should NOT be used here if 
        GREF was run using Bijvoet difference magnitudes as " FOBS", as the 
        phases on the file are then shifted by 90 degrees relative to their 
        true values. (See GREF writeup).
         
        The output file is binary and is suitable for input to FSFOUR.
        Each record contains
        
        H, K, L, FOM*FPH, FOM*FP, PHICALC
        
        where the indices are INTEGERS, the other quantities REALS and PHICALC 
        is in degrees.  The figure of merit and phase come from the phased 
        file while FPH and FP come from the derivative data file.